9XVQ | pdb_00009xvq

Crystal structure of the NFIA-N0 DNA complex

• PDB DOI: https://doi.org/10.2210/pdb9XVQ/pdb

• Classification: DNA BINDING PROTEIN/DNA
• Organism(s): Homo sapiens, synthetic construct
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2025-11-26 Released: 2025-12-24 
• Deposition Author(s): Pan, S.L., Min, J.R., Liu, K.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.76 Å
• R-Value Free: 
  0.222 (Depositor), 0.218 (DCC) 
• R-Value Work: 
  0.195 (Depositor), 0.195 (DCC) 
• R-Value Observed: 
  0.196 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of the NFIA-N0 DNA complex

Pan, S.L., Min, J.R., Liu, K.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: native gel electrophoresis

Macromolecule Content 

• Total Structure Weight: 31.6 kDa 
• Atom Count: 1,927 
• Modeled Residue Count: 178 
• Deposited Residue Count: 247 
• Unique protein chains: 1
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Nuclear factor 1 A-type	A	230	Homo sapiens	Mutation(s): 0  Gene Names: NFIA, KIAA1439
UniProt & NIH Common Fund Data Resources
Find proteins for Q12857 (Homo sapiens) Explore Q12857  Go to UniProtKB:  Q12857
PHAROS:  Q12857 GTEx:  ENSG00000162599

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*AP*AP*GP*TP*TP*GP*GP*CP*AP*TP*GP*CP*CP*AP*AP*CP*TP*T)-3')	B	17	synthetic construct

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN (Subject of Investigation/LOI)	C [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.76 Å
• R-Value Free:  0.222 (Depositor), 0.218 (DCC) 
• R-Value Work:  0.195 (Depositor), 0.195 (DCC) 
• R-Value Observed: 0.196 (Depositor) 

Space Group: I 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 48.501	α = 90
b = 113.243	β = 90
c = 128.117	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
XDS	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-12-24 
Deposition Author(s): Pan, S.L., Min, J.R., Liu, K.

---

Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	32371328

Revision History  

• Version 1.0: 2025-12-24
  Type: Initial release